Sorting the cbioportal web output of oncoprint based on frequency percentage

Question

[ivivek_ngs]

Hi,

I am trying to run a data of 105 genes (combined SNP,INDEL,CNV) in the cbioportal webpage to understand how these genes are affected across Ovarian serous cystadenocarcinoma data(Nature, 2011). First of all I cannot do it for more than 100 genes. So I split the list in 2. But most improtantly I see that I cannot download the oncoprint image in pdf. It seems it does not work. If I try to mess much with the page clicking different option it crashes most of the time. I can only download in SVG format as of now. I would like to ask that can the sorting be done based on the frequency percentage? If that is possible how can that be done? I f I try to drag the genes with high frequency percentage up to the top the page crashes. I have tried in Mozilla and Chrome. Pages are either crashing or becoming unresponsive. I do not see that option in the webpage. Any help appreciated

Regards

Answer 1

[JJ Gao]

• There is some technical issues for downloading large PDF files, please use SVG and convert to PDF using tools such as Adobe Illustrator.
• There is no functions for sorting genes on cBioPortal. I would suggest to get the percentage first and then copy the results of alteration percentages per gene in the Download tab and sort them in a spreadsheet. Then you could do another query with genes sorted by alteration frequency.

[ivivek_ngs]

Thanks , I actually did that with my genes. Yes I was lucky that the pdf download worked for me yesterday. There is more issue with Firefox than Chrome, this I would like to point out.